For better or for worse, Bubble seems to automatically give focus to what it determines to be the “first” input available. In my experience, simply rearranging inputs will cause the auto-focused one to change.

If the aim is to not have anything appear to have focus when the popup appears, one [janky] work-around would be to add an input (such as a checkbox) at the top of the popup (and not nested in a group or anything) and then cover it up with a “bandaid” (such as a Shape element) whose color matches the background of the popup.